. . . M a c S t A n R e a d M e . . .
MacStAn: stands for Macintosh Structural Analysis.
from
F. U. Gast
E-mail gast@vms.biochem.mpg.de
What it does:
1. Generation of random sequences. You can change the G+C
content, hold up to three portions constant, and limit the
length of monotonous base strings. In another option, you can
preset the entire composition of the 16 dinucleotides, or you
can shuffle an original sequence. You can also enter new or edit
existing sequences, save, print, cut, copy, paste, etc.
2. Whimpy (i. e. no computation of energies) "combinatorial"
secondary structure analysis of nucleic acids; one thing the
nice programs MacVector and DNA Strider can't. It is relatively
stable. Together with the random sequence module, you may want
to find random sequences (longer ones or RAPD primers) with a
certain amount of secondary structure.
3. Version 1.3 has added a few new features already known from
other programs to the original version, such as import of GCG
files, "Dot Plot", "Find", "Translate", and a "View" menu which
makes a view in triplets and other groups. Version 1.7 has added
a nice "Composition" option which not only computes the mono-,
di- and trinucleotide composition as known from the GCG program
COMPOSITION, but does so also in non-overlapping frames (which
widens the possibility for sequence analysis). Version 1.8 has
added a barebones implementation for the comparison of two
sequences ("alignment").
___________________________________________________________
- The program is self-explanatory; an on-line help is included.
Since it cannot be programmed differently, the help got a
special menu; it is on the rightmost side. Please read the
information provided in this menu first before you start! It
should contain everything you need.
- Although programmed using the shoddy MS QuickBasic 1.00B (the
compiler is not even running under System 7; I had to compile
the latest versions in System 6.0.7 and then switch back to 7),
the program runs under System 7.x Qit even has a pretty System 7
color iconQ as well as under System 6. I have noticed a few
problems running under both systems, but they are minor and
impossible or not worth fixing.
- A few previous bugs have been removed, e. g. "losing track of
the temporary file" which produced program crashes before. The
program now puts the temporary file in the System Folder and
cannot lose its location unless you drag it out of the System
Folder (even then the program will continue to run).
- Also, printing is much safer now. If you choose PrintI from
the File menu, you are moved through the printer driver dialog
boxes you expect from a professional program. Since the program
has grown in size, it became impossible to print out documents
from within the program on a Mac Classic equipped with an HP
DeskWriter because of memory problems. I could print documents
on LaserWriters and the StyleWriter II with "IIsi" and IIcx"
machines. It is still possible to save the sequence and the fold
as text files and print them out with a word processor.
- Running under System 7 is one thing, full compatibility
another. I do not guarantee that it runs with 32 bit addressing,
nor do I guarantee that it runs with virtual memory switched on
(virtual memory works so far, as long as the program resides in
RAM). Moreover, it does not take advantage of the possibilities
of System 7, such as real "multitasking", Publish and Subscribe,
"AppleEvents", or other things. Also, although "drop-launching"
(dragging a document icon onto the application's icon) works, it
only starts the program, it never actually opens the document.
The reason for this is that I tried to make the program read the
low memory address of the document to open it Q since that only
produced bad system crashes in my hands, I let it be.
- I have lost data more than once when running the Talking Moose
together with my programs (which otherwise indeed works). It
happened not in just one program, it happened in all of them.
The Talking Moose is fun, but when all you write to a file is
zeros, or when the program behaves not very well and freezes up,
some conflicts are imminent. I highly recommend that you remove
any strange or unknown INITs/cdevs (for an explanation, refer to
the manual or Mac literature) from your System Folder, although
the only one that definitively crashed was the Talking Moose.
It's obviously the Moose's fault, nevertheless, it's ugly.
- You can give the programs to others, if you wish. These
programs are free of charge (I used a lot of my free time for
programming), but please mention them in your publications if
you use them. I also encourage you to send a small registration
fee.
- If you really feel inclined to use ResEdit (Apple's resource
editor, currently in version 2.1) to change the programs, one
word of caution: ResEdit is very powerful; you might change the
programs so that they are not running at all. Here are a few
suggestions: First, if you don't know for sure how to use it Q
don't use it. If you do know, try to work on a copy rather than
on the original. Don't tamper with the hex codes if you open up
the hex editor because that surely scrambles the program.
Second, the dialog boxes and pulldown menus are all
"hard-programmed", i. e. they do not use resources; you can't
change them with ResEdit (new versions of the programs will use
resources). Third, don't change the settings in ResEdit's "Get
Info..." dialog box (e. g. type and creator) or the BNDL
resource because then you will have problems with opening your
documents and seeing your icons. Fourth, since it is my work, I
request that my name is left on all copies of the program. Even
if you want to see your name in the About... dialog box, don't.
The programs are so complicated and needed so much work, that I
would consider such an action  an unfriendly act. Also, I
demand that you do not decompile the programs and/or use it in
commercial applications. If you did, I would have to sue you.
__________________________________________________________
Version history:
- Secondary structure and random sequence modules as separate,
command-driven (!) programs developed January-February 1991 -
"0.9": integration of both programs, March 1991 - first 1.0.x
versions of MacStAn with a Macintosh interface, June 1991 -1.1:
new code organization, new icons, window refreshing, more
efficient secondary structure search, more sequence conversions,
printing of diagrams possible, bug fixes, July 1991 - 1.2:
better representation of found hairpins, separate help file,
temporary file reliably placed in System folder, flag for saving
of sequences, bug fix in sequence editing, March 1992 - 1.3: new
"View" menu, Dot Plot, error handling routines, March 1992 -
1.4: new menu items: "Permute SequenceI", "Composition", April
1992 - 1.5: new items: "DinucleotidesI", "Genetic Code"
(unfinished), April 1992 - 1.6: finishing of 1.5, change of
editing of new sequences, "Delete BasesI", shortcuts, bug fixes,
April 1992 - 1.7: better window refreshing, altered Help menu
and Help file organization, elimination of most sounds due to
system crashes, bug fixes, July 1992 - 1.8: change in menu
handling, undo, comment, removal of unused program code, August
1992 - 1.8.1: GCG import, alert icons, pasting possible with CR
and space in Clipboard, better hilite of found sequences, minor
bug fixes, March 1993 - 1.8.2: new items: "CompareI", "AlignI",
menu and code rearrangements, handling of inserted sequences
created by SEQED for GCG import, new dialog for choosing of DNA
or RNA, bug fix in dinucleotides, sequence editing and Clipboard
checking, April 1993 - 1.8.3: showing of more lines of text
(600), i. e. also showing of more secondary structure helices,
more efficient limiting of 32 K text, new subroutines for
efficient code, introduction of a maximum of 32 K of random
sequence trials, release version for EMBNET, May 1993 - 1.8.4:
more text export, bug fix in random sequence dialog box,
restriction of % GC deviation for random sequences, pasting also
of small caps (i. e. better communication with other programs),
"Done" button shifted in "Dot Plot" window, more flexible "Find
SequenceI", computational inaccuracy eradicated in
"Composition", E-mail address given in credit box, June 1993 -
1.8.5: new window handling (the old window is now closed after a
new file has been selected,saving is done without a new dialog
box), "Clear Sequence", "Shuffle Sequence", translation and
composition possible for both DNA and RNA, always switching to
other programs enabled, bug fixes in Find Sequence, Align, and
in file type handling when opening sequence files, August 1993
===================================================================
Coming up: CurvPlot, a curve analysis for rotational diffusion
and other experiments.
If you have recorded experimental (mainly exponential) curves
with a digitizer, this program is for you. It can manipulate
(scale, normalize, smooth, add, etc.) digitizer data and analyze
them (integration, linear regression, exponential decay), all
with a full Mac interface. It has been successfully applied to
the analysis of transient electric birefringence experiments -
where you can watch the tumbling of elongated molecules like
DNA.
This program already exists in version 2.3.6, but I'd like to
rewrite it to make it even more flexible.